Description

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', taxid:'6973' ]

assembly (file)

assembly fasta file

database (file)

Files of the database downloaded from the ncbi server, https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/. All files of one db should be downloaded and given to the process as channel.collect(). The link contains 2 databases, test-only and all. Use all for pipeline usage and test-only for tests.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', taxid:'9606' ]

versions (file)

File containing software versions

versions.yml

fcs_gx_report (file)

Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)

*.fcs_gx_report.txt

taxonomy_report (file)

Report containing the contig identifier and mapped contaminant species

*.taxonomy.rpt
author
Github user tillenglert
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Tools

fcs
United States Government Work

"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."

ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools github.com/ncbi/fcs/wiki/FCS-GX https://github.com/ncbi/fcs